I'm busy with genome-guided transcriptome assembly of some Illumina data from human. I used STAR for read mapping on hg19 and cufflinks for transcriptome assembly. I performed the analysis for two independent datasets, separately (one single end, 36bp and another, paired-end 100 bp). After conversion of "transcripts.gtf" file produced by cufflinks to fasta file, I observed that the count of sequences in fasta files related to the two independent datasets is the same. I was wondering if it is normal or something is wrong?
Thanks in advance